Capcom has since responded to the allegations with something most wouldn't hesitate to label a bit too murky for comfort. Giant Bomb has Capcom's official statement:

"Secondhand game sales were not a factor in this development decision…so we hope that all our consumers will be able to enjoy the entirety of the survival-action experiences that the game does offer…

In Resident Evil: The Mercenaries 3D, all mission progress is saved directly to the Nintendo 3DS cartridge, where it cannot be reset…The nature of the game invites high levels of replayability in order to improve mission scores. In addition, this feature does not remove any content available for users."

So, data cannot be reset when stored on the Nintendo 3DS game cartridges? False. We hope we're just misinterpreting what they mean by that fact, but we know that game data can be erased on games for the Nintendo 3DS. I've confirmed this with both nintendogs + cats (what?) and The Legend of Zelda: Ocarina of Time 3D.